ArticleBMC genomics2015
Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 38 citations in OpenAlex.
- Strawberry atlas:PeerJ · 2026Article
- Comparative Transcriptomic Analysis Reveals Key Growth-Related Genes and Alternative Splicing Events in Siniperca scherzeri.Marine biotechnology (New York, N.Y.) · 2025Article
- Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice.The Plant cell · 2024Article
- Importance of pre-mRNA splicing and its study tools in plants.Advanced biotechnology · 2024Review
- Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels.International journal of molecular sciences · 2023Article
- A complete telomere-to-telomere assembly of the maize genome.Nature genetics · 2023Article
- Review
- Comparative Analysis of Alternative Splicing in Two Contrasting Apple Cultivars Defense againstInternational journal of molecular sciences · 2022Article
- Article
- In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue.PLoS genetics · 2022Article
- Analysis of Whole-Transcriptome RNA-Seq Data Reveals the Involvement of Alternative Splicing in the Drought Response ofFrontiers in genetics · 2022Article
- Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales).G3 (Bethesda, Md.) · 2021Article
- Article
- Changes in Alternative Splicing in Response to Domestication and Polyploidization in Wheat.Plant physiology · 2020Article
- QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice.Frontiers in genetics · 2020Article
- Distribution and Characteristics of Transposable Elements in the Mulberry Genome.The plant genome · 2019Article
- Article
- Increased Alternative Splicing as a Host Response to Edwardsiella ictaluri Infection in Catfish.Marine biotechnology (New York, N.Y.) · 2018Article
- Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.).BMC plant biology · 2018Article
- Genome-Wide Association Analyses Reveal the Importance of Alternative Splicing in Diversifying Gene Function and Regulating Phenotypic Variation in Maize.The Plant cell · 2018Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement.
resultsIn maize and teosinte, 13,593 highly conserved genes, including 12,030 multiexonic genes, were detected. By identifying AS isoforms from mutliexonic genes, we found that AS types were not significantly different between maize and teosinte. In addition, the two main AS types (intron retention and alternative acceptor) contributed to more than 60% of the AS events in the two species, but the average unique AS events per each alternatively spliced gene in maize (4.12) was higher than that in teosinte (2.26). Moreover, 94 genes generating 98 retained introns with transposable element (TE) sequences were detected in maize, which is far more than 9 retained introns with TEs detected in teosinte. This indicates that TE insertion might be an important mechanism for intron retention in maize. Additionally, the AS levels of 3864 genes were significantly different between maize and teosinte. Of these, 151 AS level-altered genes that are involved in transcriptional regulation and in stress responses are located in regions that have been targets of selection during maize improvement. These genes were inferred to be putatively improved genes.
conclusionsWe suggest that both maize and teosinte share similar AS mechanisms, but more genes have increased AS complexity during domestication from teosinte to maize. Importantly, a subset of AS level-increased genes that encode transcription factors and stress-responsive proteins may have been selected during maize improvement.
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